Journal Articles
| Authors | Article Title | Journal | Published Year | Status | DOI |
|---|---|---|---|---|---|
| Radomir M. Slominski, Chander Raman, Jake Y. Chen, and Andrzej T. Slominski | How cancer hijacks the body’s homeostasis through the neuroendocrine system and why | 2022 | in review | ||
| Andrzej T. Slominski, Radomir M. Slominski, Chander Raman, Jake Y. Chen, Mohammad Athar, Craig Elmets | Neuroendocrine signaling in the skin with a special focus on the epidermal neuropeptides | American Journal of Physiology-Cell Physiology | 2022 | in review | |
| Min Gao, Shanrun Liu, Qi Wu, PingAr Yang, Alex Essman, Bao Luo, Oluwagbemiga A. Ojo, David Crossman, Michael R. Crowley, Ignacio Sanz, Jake Y. Chen, W. Winn Chatham, John D. Mountz*, and Hui-Chen Hsu* | High Dimensional Analysis Reveals IL-4R as a Protective Factor to Prevent DN2 B-cell Development in SLE | Immunology | 2021 | in review | |
| Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, and Jake Y. Chen | Guest Editorial for Selected Papers from BIOKDD 2021 | IEEE/ACM Transactions on Computational Biology and Bioinformatics | 2022 | in press | |
| Dongmei Sun, Thanh M. Nguyen, Robert J. Allaway, Jelai Wang, Verena Chung, Thomas V Yu, Michael Mason, Isaac Dimitrovsky, Lars Ericson, Hongyang Li, Yuanfang Guan, Ariel Israel, Alex Olar, Balint Armin Pataki, RA2 DREAM Challenge Community, Gustavo Stolovitzky, Justin Guinney, Percio S. Gulko, Mason B. Frazier, James C. Costello*, Jake Y. Chen*, and S. Louis Bridges, Jr.* | A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis | JAMA Network Open, 5(8):e2227423 | 2022 | published | 10.1001/jamanetworkopen.2022.27423 |
| Christian T. Stackhouse, Joshua C. Anderson, Zongliang Yue, Thanh Nguyen, Nicholas J. Eustace, Lara Ianov, Catherine P. Langford, Jelai Wang, James R. Rowland III, Chuan Xing, Fady M. Mikhail, Eddy S. Yang, Anita B. Hjelmeland, C. Ryan Miller, Jake Y. Chen, G. Yancey Gillespie, Christopher D. Willey | A Novel in vivo Model of Glioblastoma Radiation Resistance Identifies Long Non-coding RNAs and Targetable Kinases, | JCI Insights, 7(16):e148717 | 2022 | published | doi.org/10.1172/jci.insight.148717 |
| Zhenyu Weng, Zongliang Yue, Yuesheng Zhu, and Jake Y. Chen* | DEMA: a Distance-bounded Energy-field Minimization Algorithm to Model and Layout Bio-molecular Networks with Quantitative Features. | Bioinformatics, Vol. 38, No. S1, ppi359–i368, | 2022 | published | doi.org/10.1093/bioinformatics/btac261 |
| Jianyi Zhang*, Yuji Nakada, Yang Zhou, Wuming Gong, Eric Zhang, Erik Skie, Thanh Nguyen, Yuhua Wei, Meng Zhao, Wangping Chen, Jake Y. Chen, Gregory Walcott, Daniel Garry, Jiacheng Sun, and Syed Raza | Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time-window of Cardiomyocyte Proliferation and Myocardial Regeneration. | Circulation, No. 145, pp. 1744-1747 | 2022 | published | |
| Zongliang Yue, Radomir Slominski, Samuel Bharti, and Jake Y Chen* | PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool of High-throughput Functional Genomics Results. | Frontiers in Genetics, Vol. 13, | 2022 | published | doi.org/10.3389/fgene.2022.820361 |
| Thanh Nguyen, Jacob Jeevan, Nuo Xu, and Jake Y. Chen*. | Polar Gini Curve: a Quantitative Technique to Discover Gene Expression Spatial Patterns from Single-cell Data. | Genomics, Proteomics, and Bioinformatics, | 2022 | published | doi.org/10.1016/j.gpb.2020.09.006 |
| Carlene L. Zindl, Steven J. Witte, Vincent A. Laufer, Min Gao, Zongliang Yue, Karen M. Janowski, Baiyi Cai, Blake F. Frey, Daniel J. Silberger, Stacey N. Harbour, Duy Pham, Henrietta Turner, Fran E. Lund, Bruce A. Vallance, Alexander F. Rosenberg, Trenton R. Schoeb, Jake Y. Chen, Robin T. Hatton and Casey T. Weaver* | A Non-redundant Role for T cell-derived IL-22 in Antibacterial Defense of Colonic Crypts | Immunity. Vol. 55, No. 3, pp. 494-511.e11 | 2022 | published | |
| Thanh Minh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D Willey and Jake Y Chen* | Statistical Enrichment Analysis of Samples (SEAS): a General-purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. | Frontiers in Big Data, Vol. 4, No. 81 | 2021 | published | doi.org/10.3389/fdata.2021.725276 |
| D. Yan*, S. Thankachan and Jake Y. Chen* | Guest Editorial for Selected Papers From BIOKDD 2019. | IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 18, No. 3, pp. 809-810. | 2021 | published | doi.org/10.1109/TCBB.2021.3067071 |
| Sweta B. Patel, Travis Nemkov, Davide Stefanoni, Gloria A. Benavides, Brittany L. Crown, Victoria R. Matkins, Virginia Camacho, Ashley T. Hoang, Danielle E. Tenen, Samuel L. Wolock, Jihye Park, Mahmoud A. Bassal, Li Ying, Zongliang Yue, Jake Y. Chen, Henry Yang, Daniel G. Tenen, Paul Brent Ferrell, Rui Lu, Victor Darley-Usmar, Angelo D’Alessandro, Ravi Bhatia, Robert S. Welner | Metabolic alterations mediated by STAT3 promotes drug persistence in CML. | Leukemia, Vol. 35, pp. 3371–3382. | 2021 | published | |
| Andrzej T Slominski, Tae-Kang Kim, Shariq Qayyum, Yuwei Song, Zorica Janjetovic, Allen SW Oak, Radomir M Slominski, Chander Raman, Joanna Stefan, Carlos A Mier-Aguilar, Venkatram Atigadda, David K Crossman, Andriy Golub, Yaroslav Bilokin, Edith K Y Tang, Jake Y. Chen, Robert C Tuckey, Anton M Jetten, Yuhua Song | Vitamin D and Lumisterol Derivatives Can Act on Liver X Receptors (LXRs), | Scientific Reports, Vol. 11, No. 1:8002. | 2021 | published | |
| Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan*, and Jake Y. Chen*. | Linking Clinotypes to Phenotypes and Genotypes from Laboratory Test Results in Comprehensive Physical Exams. | BMC Medical Informatics and Decision Making, Vol. 21, Suppl 3: 51 | 2021 | published | doi.org /10.1186/s12911-021-01387-z |
| Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Dang, and Jake Y. Chen* | PAGER-CoV: A Comprehensive Collection of Pathways, Annotated-gene-lists, and Gene Signatures for Coronavirus Disease Studies. | Nucleic Acids Research, Vol. 49, No. D1 | 2021 | published | doi.org/10.1093/nar/gkaa1094 |
| Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, and Jake Y. Chen | Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System | ACM/IEEE Transactions on Computational Biology and Bioinformatics, Vol. 18, No. 2, pp. 731-744 | 2021 | published | doi.org/10.1109/TCBB.2019.2920912 |
| C.D. Willey, C.T. Stackhouse, J.R. Rowland, C.P. Langford, J.C. Anderson, L. Ianov, Z. Yue, T. Nguyen, A.B. Hjelmeland, Jake Y. Chen, G.Y. Gillespie | Multi-omic Exploration of Inherent and Acquired Radiation Resistance of Glioblastoma Patient-derived Xenografts | International Journal of Radiation Oncology Biology Physics, Vol. 108, No. 3, Suppl., pp. S40. | 2020 | published | |
| Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, and Gregory P Walcott. | Identifying the Key Regulators that Promote Cell-cycle Activity in the Hearts of Early Neonatal Pigs after Myocardial Injury. | PLOS ONE | 2020 | published | doi.org/10.1371/journal.pone.0232963 |
| Keshav K Singh, Gyneshwer Chaubey, Jake Y. Chen, and Prashanth Suravajhala. | Decoding SARS-CoV-2 Hijacking of Host Mitochondria in Pathogenesis of COVID-19 | American Journal of Physiology-Cell Physiology | 2020 | published | doi.org/10.1152/ajpcell.00224.2020 |
| Huixian Hong, Min Gao, Qi Wu, PingAr Yang, Shanrun Liu, Hao Li, Peter D. Burrows, Daniel Cua, Jake Y. Chen, Hui-Chen Hsu, and John D. Mountz. | IL-23 promotes a coordinated B-cell germinal center program for class-switch recombination to IgG2b in BXD2 mice | J. Immunology, Vol. 205(2), pp 346-358 | 2020 | published | |
| Da Yan, Xin Gao, Samah J. Fodeh, and Jake Y. Chen* | Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018. | IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 17, No. 6, pp. 1832-1834. | 2020 | published | |
| Syed A Muhammad, Hiba Ashfaq, Sidra Zafar, Fahad Munir, Muhammad B Jamshed, Jake Y. Chen, and Qiyu Zhang | Polyvalent Therapeutic Vaccine for Type 2 Diabetes Mellitus: Immunoinformatics Approach to Study Co-Stimulation of Cytokines and GLUT1 Receptors. | BMC Molecular and Cell Biology, Vol. 21(1):56 | 2020 | published | doi.org/10.1186/s12860-020-00279-w |
| George Dobbins, Amit Patki, Dongquan Chen, Hemant K. Tiwari, Curtis Hendrickson, William J. Britt, Karen Fowler, Jake Y. Chen, Suresh B Boppana, and Shannon A Ross*. | Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection. | BMC Infectious Disease, Vol. 19(1);1046 | 2019 | published | doi.org/10.1186/s12879-019-4681-0 |
| Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, and Jake Y. Chen* | Weighted in-Path Edge Ranking for Biomolecular Association Networks | Quantitative Biology, Vol. 7, pp 313-326. | 2019 | published | |
| Zongliang Yue, Christopher D Willey, Anita B Hjelmeland, and Jake Y. Chen* | BEERE: a Web Server for Biomedical Entity Expansion, Ranking, and Explorations. | Nucleic Acids Research, gkz428 | 2019 | published | |
| Xiaowen Liu, Zongliang Yue, Yimou Cao, Lauren Taylor, Qing Zhang, Sung Wong Choi, Samir Hanash, Sawa Ito, Jake Y. Chen, Huanmei Wu, and Sophie Paczesny | A GVHD-free Antitumoral Signature Following Allogeneic Donor Lymphocyte Injection Identified by Proteomics and Systems Biology. | JCO Precision Oncology, Vol. 3, pp 1-11 | 2019 | published | |
| Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, and Nengjun Yi | Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. | BMC Bioinformatics, Vol. 20, p. 94. | 2019 | published | doi.org/10.1186/s12859-019-2656-1 |
| Syed Aun Muhammad*, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, and Jake Y. Chen* | A Systematic Simulation-based Meta-analytical Framework for Prediction of Physiological Biomarkers in Alopecia. | Journal of Biological Research-Thessaloniki, Vol. 26, No. 2 | 2019 | published | doi.org/10.1186/s40709-019-0094-x |
| Xin Gao, Jake Y. Chen, and Mohammed J. Zaki | Multiscale and Multimodal Analysis for Computational Biology. | IEEE/ACM Transactions on Computational Biology and Bioinformatics | 2018 | published | |
| Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen* | “Super Gene Set” Causal Relationship Discovery from Functional Genomics Data. | ACM/IEEE Transactions on Computational Biology and Bioinformatics, Vol. 15, No. 6, pp. 1991-1998. | 2018 | published | |
| Wuqiang Zhu, Eric Zhang, Meng Zhao, Zechen Chong, Chengming Fan, Yawen Tang, Jervaughn D. Hunter, Anton V. Borovjagin, Greggory P. Walcott, Jake Y. Chen, Gangjian Qin, Jianyi Zhang | Regenerative Potential of Neonatal Porcine Hearts. | Circulation, Vol. 138, No. 24, pp. 2809-2816. (IF = 18.88) | 2018 | published | |
| Syed Aun Muhammad*, Jinlei Guo, Thanh Minh Nguyen, Xiaogang Wu, Baogang Bai, X Frank Yang, Jake Y. Chen* | Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins | Frontiers in Microbiology, Vol. 9, No. 380 | 2018 | published | doi.org/10.3389/fmicb.2018.00380 |
| Zongliang Yue, Qi Zheng, Micheal T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen* | PAGER 2.0: An Update to the Pathway, Annotated-list, and Gene-signature Electronic Repository for Network Biology | Nucleic Acids Research, Vol. 46, No. D1, pp. D668-D676 | 2018 | published | |
| Zongliang Yue, Itika Arora, Eric Zhang, Vincent Laufer, S. Louis Bridges, and Jake Y. Chen* | Repositioning Drugs by Targeting Network Modules: A Parkinson’s Disease Case Study | BMC Bioinformatics, Vol. 18, Suppl 14, 532. | 2017 | published | |
| Baron Arnone, Jake Y. Chen, and Gangjian Qin | Characterization and Analysis of Long Non-Coding RNA (lncRNA) in in vitro- and ex vivo-derived Cardiac Progenitor Cells | PLOS ONE | 2017 | published | |
| Vincent A. Laufer, Jake Y. Chen, S Louis Bridges Jr | Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases. | Rheumatic Disease Clinics, Vol. 43, No. 3, pp. 449-466. | 2017 | published | |
| Jake Y. Chen*, Ragini Pandey, and Thanh Nguyen | HAPPI-2: Constructing a Comprehensive Map of Human Annotated and Predicted Protein Interactions | BMC Genomics, Vol. 18, 182. (IF = 4.07) | 2017 | published | |
| Syed Aun Muhammad*, Waseem Raza, Thanh Nguyen, Baogang Bai, Xiaogang Wu, and Jake Chen* | Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus. | Frontiers in Physiology, Vol. 8, No. 13, | 2017 | published | doi.org/10.3389/fphys.2017.00013 |
| Fan Zhang and Jake Y. Chen* | A Method for Identifying Discriminative Isoform-Specific Peptides for Clinical Proteomics Application. | BMC Genomics, Vol. 17, Suppl. 7, 522. | 2016 | published | |
| Xiaowen Liu, Zongliang Yue, Jeffrey Yu, Etienne Daguindau, KushiKushekhar, Qing Zhang, Yuko Ogata, Philip Gafken, Yoshihiro Inamota, Adam Gracon, David Wikes, John Hansen, Stephanie Lee, Jake Y. Chen, and Sophie Paczesny* | Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation | American Journal of Transplantation, Vol. 16, No. 8, pp. 2342-2351. | 2016 | published | |
| Syed Aun Muhammad, Nighat Fatima, Nawazish-i-Husain Syed, XiaogangWu, X. Frank Yang, and Jake Y. Chen* | MicroRNA Expression Profiling of Human Respiratory Epithelium Affected by Invasive Candida infection | PLOS ONE, Vol. 10, No. 8, e0136454 | 2015 | published | |
| Zongliang Yue, Madhura Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael Neylon, Liugen Zhu, Timothy Ratliff, and Jake Y. Chen* | PAGER: Constructing PAGs and new PAG-PAG Relationships for Network Biology. | Bioinformatics, Vol. 31, No. 12, pp. i250-i257 | 2015 | published | |
| Hui Huang, Thanh Nguyen, Sara Ibrahim, and Jake Y. Chen* | DMAP: A next-generation connectivity map database towards drug repositioning applications. MCBIOS ’15 Special Issue | BMC Bioinformatics, Vol. 16, Suppl. 13, S4 | 2015 | published | |
| Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen* | A Method for Developing Regulatory Gene Set Networks to Characterize Complex Biological Systems. | BMC Genomics, Vol. 16, Suppl. 11, S4 | 2015 | published | |
| Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki | Knowledge Discovery Using Big Data in Biomedical Systems. | IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, No. 4, pp. 726-729. | 2015 | published | |
| Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, and Jake Y. Chen* | SLDR: A Computational Technique to Identify Novel Genetic Regulatory Relationship. | BMC Bioinformatics, Vol. 15, Suppl. 11, S1 | 2014 | published | |
| Syed Aun Muhammad, Safia Ahmed, Amjad Ali, Hui Huang, Xiaogang Wu, X. Frank Yang, Anam Naz, Jake Y. Chen* | Prioritizing Drug Targets in Clostridium botulinum with a Computational Systems Biology Approach. | Genomics, Vol. 104, No. 1, pp. 24-35 | 2014 | published | |
| Xiaogang Wu, Mohammad Al Hasan, and Jake Y. Chen* | Pathway and Network Analysis in Proteomics | Journal of Theoretical Biology, Vol. 362, pp. 44-52 | 2014 | published | |
| Zongliang Yue, Zhan Xie, Ping Wan, and Jake Y. Chen | Computational Identification of De-centric Genetic Regulatory Relationships from Functional Genomic Data, | Lecture Notes in Bioinformatics, Vol. 8492, pp. 224-235. | 2014 | published | |
| Tianxiao Huan, Xiaogang Wu, Zengliang Bai*, and Jake Y. Chen* | Seed-weighted Random Walk Ranking for Cancer Biomarker Prioritization: a Case Study in Leukemia. | International Journal of Data Mining and Bioinformatics, Vol. 9, No. 2, pp.135-148. | 2014 | published | |
| Shubo Zhang, Jake Y. Chen, Jianan Rao, Shanghong Zhang, Daniel Wai Tin Chan, Guanghua Liu, Yang Xu, and Miao He | Genetic Variation Analysis of Hemagglutinin and Neuraminidase of Human Influenza A (H3N2) Virus in Hong Kong (1997-2006). | African Journal of Microbiology Research, Vol. 8, No. 18, pp. 1863-1898. | 2014 | published | |
| Jake Y. Chen, Micheline Piquette-Miller, and BP Smith | Network Medicine: Finding the Links to Personalized Therapy | Clinical Pharmacology & Therapeutics, Vol. 94, No. 6, pp. 613-615. | 2013 | published | |
| Fan Zhang, Jake Chen, Mu Wang, and Renee Drabier | A Neural Network Approach to Multi-biomarker Panel Discovery by High-throughput Plasma Proteomics Profiling of Breast Cancer. | BMC Proceedings, Vol. 7, Suppl. 7, S10 | 2013 | published | |
| Huajun Chen*, Tong Yu*, and Jake Y. Chen* | Semantic Web Meets Integrative Biology: A Survey. | Briefings in Bioinformatics, Vol. 14, No. 1, pp. 109-125. | 2013 | published | |
| Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen* | Predicting Adverse Drug Reaction Profiles by Integrating Protein Interaction Networks with Drug Structures. | Proteomics, Vol. 13, No. 2, pp. 313-324 | 2013 | published | |
| Fan Zhang and Jake Y. Chen* | Breast Cancer Subtyping from Plasma Proteins. | BMC Medical Genomics, Vol 6, Suppl. 1, S6 | 2013 | published | |
| Hui Huang, Xiaogang Wu, Ragini Pandey, Jiao Li, Guoling Zhao, Sara Ibrahim, Jake Y. Chen* | C2Maps: A Network Pharmacology Database with Comprehensive Disease-Gene-Drug Connectivity Relationships. | BMC Genomics, Vol. 13, Suppl. 6, S17. | 2012 | published | |
| Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan*, Jake Y. Chen* | PAGED: A Pathway and Gene-set Enrichment Database to Enable Molecular Phenotype Discoveries. | BMC Bioinformatics, Vol. 13, Suppl. 15, S2. (IF = 2.75) | 2012 | published | |
| Paul Hale, Alfredo M. López-Yunez, Jake Y. Chen* | Genome-wide Meta-analysis of Genetic Susceptible Genes for Type-2 Diabetes | BMC Systems Biology, Vol. 6, Suppl. 3, S16 | 2012 | published | |
| Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li*, and Jake Y. Chen* | Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays. | Journal of Integrative Bioinformatics, Vol. 9, No. 2, 213. | 2012 | published | |
| John Springer, Fan Zhang, Peter Hussey, Charles Buck, Fred Regnier, and Jake Y. Chen* | Towards a Metadata Model for Mass-Spectrometry Based Clinical Proteomics. | Current Bioinformatics, Vol. 7, No. 3, pp. 246-254. | 2012 | published | |
| Mohammad Al Hasan, Jun Huan, Jake Chen, and Mohammed J. Zaki | Biological Knowledge and Data Mining: An Editorial | Scientific Programming, Vol. 20, No. 1, pp. 1-2. | 2012 | published | |
| Liang-Chin Huang, Xiaogang Wu, and Jake Y. Chen* | Predicting Adverse Side Effects of Drugs. | BMC Genomics, Vol. 12, Suppl. 5, S11. | 2011 | published | |
| Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, and Jake Y. Chen* | Reordering Based Integrative Expression Profiling for Microarray Classification. | BMC Bioinformatics, Vol. 13, Suppl. 2, S1 | 2011 | published | |
| Jiliang Li, Fan Zhang, and Jake Y. Chen* | An Integrated Proteomics Analysis of Bone Tissues in Response to Mechanical Stimulation. | BMC Systems Biology, Vol. 5, Suppl. 3, S7. | 2011 | published | |
| Fan Zhang and Jake Y. Chen* | HOMER: A Human Organ-specific Molecular Electronic Repository. | BMC Bioinformatics, Vol. 12, Suppl. 10, S4. | 2011 | published | |
| Fengjun Li, Xukai Zou, Peng Liu, and Jake Y. Chen* | New Threats to Health Data Privacy. | BMC Bioinformatics, Vol. 12, Suppl. 12, S7 | 2011 | published | |
| Lijie Sun, Hong-Mei Li, Manfredo J. Seufferheld, Kent Walters, Venu Margam, Amber Jannasch, Naomi Diaz, Catherine P. Riley, Weilin Sun, Yueh-Feng Li, William M. Muir, Jun Xie, Jing Wu, Fan Zhang, Jake Y. Chen, Eric L. Barker, Jiri Adamec, & Barry R. Pittendrigh | Systems-scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine. | PLOS ONE, 6(4): e18215 | 2011 | published | |
| Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, and Jake Y. Chen* | Computational Analysis of Drought-stress Associated miRNAs and miRNA Co-regulation Network in Physcomitrella Patens | Bioinformatics, Genomics, and Proteomics, Vol. 9, No. 1-2, pp. 37-44. | 2011 | published | |
| Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Sharon A. Meyer, Edward J. Perkins, and Jake Y. Chen* | A new Approach to Construct Pathway Connected Networks and Its Application in Dose Responsive Gene Expression Profiles of Rat Liver Regulated by 2,4DNT. | BMC Genomics, Vol. 11, Suppl. 3, S4. | 2010 | published | |
| Fan Zhang and Jake Y. Chen* | Discovery of Pathway Biomarkers from Coupled Proteomics and Systems Biology Methods. | BMC Genomics, Vol. 11, Suppl. 2, S12 | 2010 | published | |
| Ao Zhou, Fan Zhang, and Jake Y. Chen* | PEPPI: A Peptidomic Database of Human Protein Isoforms for Proteomics Experiments. | BMC Bioinformatics, Vol. 11, Suppl. 6, S7 | 2010 | published | |
| Steve Naylor and Jake Y. Chen* | Unraveling Human Complexity and Disease with Systems Biology and Personalized Medicine. | Personalized Medicine, Vol. 7, No. 3, pp. 275-289. | 2010 | published | |
| Tianxiao Huan, Xiaogang Wu, and Jake Y. Chen* | Systems Biology Visualization Tools for Drug Target Discovery. | Expert Opinion on Drug Discovery, Vol. 5, No. 5, pp. 425-439. | 2010 | published | |
| Hong-Mei Li, Lijie Sun, Omprakash Mittapalli, William M. Muir, Jun Xie, Jing Wu, Brandon J. Schemerhorn, Amber Jannasch, Jake Y. Chen, Fan Zhang, Jiri Adamec, Larry L. Murdock, and Barry R. Pittendrigh | Bowman-Birk Inhibitor Affects Pathways Associated with Energy Metabolism in Drosophila melanogaster | Insect Molecular Biology, Vol. 19, No. 3, pp. 303-313. | 2010 | published | |
| Stefano Lonardi and Jake Y. Chen* | Data Mining in Bioinformatics: Selected Papers from BIOKDD 2008 | IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 2, pp. 195-196. | 2010 | published | |
| Mingyi Wang and Jake Y. Chen* | A GMM-IG Framework for Selecting Genes as Expression Panel Biomarkers | Artificial Intelligence in Medicine, Vol. 48, No. 2-3, pp.75-82 | 2010 | published | |
| Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* | Discovering Novel Breast Cancer Drug Candidates from Biomedical Literature. | International Journal of Data Mining and Bioinformatics. Vol. 4, No. 3, pp.241-255. | 2010 | published | |
| Qian You, Shiaofen Fang, and Jake Y. Chen* | GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks. | Information Visualization, Vol. 9, No. 1, pp.1-12. | 2010 | published | |
| Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* | Building Disease-specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts. | PLoS Computational Biology, Vol. 5, No. 7: e1000450. | 2009 | published | |
| Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, and Jake Y. Chen* | HPD: An Online Integrated Human Pathway Database Enabling Systems Biology Studies. | BMC Bioinformatics, Vol. 10, Suppl. 11, S5 | 2009 | published | |
| Jake Y. Chen*, SudhaRani Mamidipalli, and Tianxiao Huan | HAPPI: an Online Database of Comprehensive Human Annotated and Predicted Protein Interactions. | BMC Genomics, Vol. 10, Suppl. 1, S16. | 2009 | published | |
| Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshu Zhou, and Jake Y. Chen* | Finding Fractal Patterns in Molecular Interaction Networks: a Case Study in Alzheimer’s Disease. | International Journal of Computational Biology and Drug Design, Vol. 2, No. 4, pp. 340-352. | 2009 | published | |
| Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, and Jake Y. Chen* | Semantic Graph Mining for Biomedical Network Analysis: an Overview. | Briefings in Bioinformatics, Vol. 10, No. 2, pp. 177-192. | 2009 | published | |
| Huian Li and Jake Y. Chen* | Improved Biomedical Document Retrieval System with PubMed Term Statistics and Expansions. | International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, pp. 74-85. | 2009 | published | |
| Sudipto Saha, Scott H. Harrison, and Jake Y. Chen* | Dissecting the Human Plasma Proteome and Inflammatory Response Biomarkers. | Proteomics, Vol. 9, No. 2, pp. 470-484. | 2009 | published | |
| Jake Y. Chen, Mohammed Zaki, and Stefano Lonardi | BIOKDD 2008: A Workshop Report on Data Mining in Bioinformatics. | SIGKDD Explorations, Vol. 10, No. 2, pp. 51-53. | 2008 | published | |
| Tianxiao Huan, Andrey Sivachenko, Scott H. Harrison, and Jake Y. Chen* | ProteoLens: a Visual Analytic Tool for Multi-scale Database-driven Biological Network Data Mining. | BMC Bioinformatics, Vol. 9, S5, pp. 1-13 | 2008 | published | |
| Sudipto Saha, Scott H. Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J. Arnold, Xiang Zhang, and Jake Y. Chen* | HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals. | BMC Medical Genomics, 2008, Vol. 1, 12. (IF = 2.66) | 2008 | published | |
| Stefano Lonardi and Jake Y. Chen* | International Workshop on Data Mining in Bioinformatics (BIOKDD) 2007: Introduction. | Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6, pp. v-vi. | 2008 | published | |
| Lee W. Ott, Katheryn A. Resing, Alecia W. Sizemore, Joshua W. Heyen, Ross R. Cocklin, Nathan M. Pedrick, H. Cary Woods, Jake Y. Chen, Mark G. Goebl, Frank A. Witzmann, and Maureen A. Harrington | Tumor Necrosis Factor-alpha and Interleukin-1 Induced Cellular Responses: Coupling Proteomic and Genomic Information. | Journal of Proteome Research, Vol. 6, Issue 6, pp. 2176-2185. | 2007 | published | |
| Lavanya Dhanapalan and Jake Y. Chen* | A Case Study of Integrating Protein Interaction Data using Semantic Web Technology. | International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 286-302. | 2007 | published | |
| Jake Y. Chen*, Zhong Yan, Changyu Shen, Dawn P. G. Brown, and Mu Wang | A Systems Biology Approach to The Study of Cisplatin Drug Resistance In Ovarian Cancers. | Journal of Bioinformatics and Computational Biology, Vol. 5, Issue 02A, pp. 383-405. | 2007 | published | |
| Megan Sickmeier, Justin Hamilton, Tanguy LeGall, Vladimir Vacic, Marc Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir Uversky, Zoran Obradovic, A Keith Dunker | DisProt: The Database of Disordered Proteins | Nucleic Acids Research, Vol. 35 (Database issue): pp. 786-93. | 2007 | published | |
| Tharam S. Dillon, Elizabeth Chang, Amandeep S. Sidhu, and Jake Y. Chen* | Ontologies for Bioinformatics I. | International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 261-267. | 2007 | published | |
| Zsuzsanna Dosztányi, Jake Y. Chen, A. Keith Dunker, István Simon, and Peter Tompa | Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution, | Journal of Proteome Research, Vol. 5, Issue 11, pp. 2985-2995 | 2006 | published | |
| Changyu Shen, Lang Li, Jake Y. Chen* | A Statistical Framework to Discover True Associations from Multi-protein Complex Pull-down Proteomics Data Sets. | Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 2, pp. 436-43. | 2006 | published | |
| Jake Y. Chen* and Andrey Y. Sivachenko | Data Mining in Protein Interactomics. | IEEE Magazine in Biology and Medicine, Vol. 24, No. 3, pp. 95-102. | 2005 | published | |
| Susie Stephens, Jake Y. Chen, Marcel Davidson, Shiby Thomas, and Barry M. Trute | Oracle Database 10g: A Platform for BLAST Search and Regular Expression Pattern Matching in Life Sciences | Nucleic Acids Research, Vol. 33, Database Issue, pp. 675-679. | 2005 | published | |
| Susie Stephens, Jake Y. Chen, and Shiby Thoma | ODM BLAST: Sequence Homology Search in the RDBMS. | IEEE Data Engineering Bulletin, Vol. 27, Issue 3, pp. 20-23 | 2004 | published | |
| Jake Y. Chen* | Book Review: Digital Code of Life—How Bioinformatics is Revolutionizing Science, Medicine, and Business. | Briefings in Bioinformatics, Vol. 5, Issue 3, pp. 305-307. | 2004 | published | |
| Jake Y. Chen* and John Carlis | Genomic Data Modeling. | Information Systems, Vol. 28, Issue 4: (Special Issue on Data Management in Bioinformatics), pp. 287-310. | 2003 | published |
Conference or Workshop Proceedings Articles
| Authors | Article Title | Conference or Workshop | Published Year | Status | DOI |
|---|---|---|---|---|---|
| Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, and Sidharth Kumar | GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web, Proceedings of Eurographics Symposium on Parallel Graphics and Visualization | 2022 | in press | ||
| James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John D. Osborne, Amy Y. Wang, S. Louis Bridges, Jr., Matt Wyatt, and Jake Y. Chen* | Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE) | Proceedings of the IEEE 21st International Conference on Information Reuse and Integration for Data Science (IRI), Las Vegas, NV, USA, 2020 pp. 194-200 | 2020 | published | 10.1109/IRI49571.2020.00035. |
| Jake Chen*, Michael Neylon, Zongliang Yue, Thanh Nguyen, Timothy Ratliff | Towards Constructing “Super Gene Sets” Regulatory Networks | Proceedings of the 2016 International Conference on Bioinformatics & Biomedicine, Shenzhen, China, | 2016 | published | 10.1109/BIBM.2016.7822534 |
| Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguen, and Jake Chen* | Predictive and Preventive Models for Diabetes Prevention using Clinical Information in Electronic Health Record | Proceedings of the 2015 International Conference on Bioinformatics & Biomedicine, Washington, DC, pp. 867-874. | 2015 | published | |
| Thanh Nguyen, Junjie Chen, Dongxiang Ji, Xiaoru Sun, Chuandi Pan,* Chengshui Chen*, and Jake Y. Chen* | An Integrated Machine Learning and Network Analysis to Discover Marker Clinical Measurement in Lung Cancer | Proceedings of 2015 International Conference on Genome Medicine, eds. Le L & Pham S, Ho Chi Minh City, Viet Nam. | 2015 | published | |
| Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen* | Constructing Regulatory Gene Set Network to Reveal Novel Insights into Biological Systems, | Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, Miami Beach, FL | 2014 | published | 10.1109/ICCABS.2014.6863927 |
| Xiaogang Wu and Jake Chen* | An Evaluation for Merging Signaling Pathways by Using Protein-Protein Interaction Data | Proceedings of IEEE International Workshop on Genomic Signal Processing and Statistics, Washington, DC | 2012 | published | |
| David Johnson, Brandon Shafer, Jaehwan John Lee, and Jake Chen* | Multi-Biomarker Panel Selection on a GPU | Proceedings of IEEE International Conference on Electro/Information Technology, Indianapolis, IN. | 2012 | published | |
| Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christopher Reinhard, Shuyu D. Li, Jake Y. Chen* | Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays | Proceedings of the Eighth Annual International Symposium on Integrative Bioinformatics, Hangfzhou, Zhejiang, China. | 2012 | published | |
| Liang-Chin Huang and Jake Y. Chen* | A Network Biology Approach to Predicting Drug Cardiotoxicity | Proceedings of the International Conference on Bioinformatics & Biomedicine, Atlanta, GA, pp. 278-281. | 2011 | published | |
| Jason McLaughlin, Qian You, Shiaofen Fang, and Jake Y. Chen* | TAO: Terrain Analytic Operators for Expert-Guided Data Mining Applications | Workshop on Visual Analytics in Healthcare, Providence, RI. | 2011 | published | |
| Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne Mckenzie, Sunil Badve, and Jake Y. Chen* | Predicting Drug Efficacy Based on the Integrated Breast Cancer Pathway Model, | IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | 2011 | published | |
| Xiaogang Wu and Jake Y. Chen* | Network Reordering Based Integrative Expression Profiling for Microarray Classification | 2011 Great Lakes Bioinformatics Conference, Athens, OH. | 2011 | published | |
| Xukai Zou*, Peng Liu*, and Jake Y. Chen* | Personal Genome Privacy Protection with Feature-based Hierarchical Dual-stage Encryptions, | 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | 2011 | published | |
| Fan Zhang and Jake Y. Chen* | Novel Protein Isoform Biomarker Identifications from Proteomes | 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | 2010 | published | |
| Hui Huang, Xiaogang Wu, Shuyu Li, Sara Ibrahim, Taiwo Ajumobi, and Jake Y. Chen* | Evaluate Drug Effects on Gene Expression Profiles with Connectivity Maps | 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | 2010 | published | |
| Fan Zhang and Jake Y. Chen* | Proteome-scale Protein Isoform Characterization with High-Performance Computing | 2010 Microsoft eScience Workshop Proceedings, Berkeley, CA. | 2010 | published | |
| Fengjun Li, Jake Y. Chen, Xukai Zou, and Peng Liu | New Privacy Threats in Healthcare Informatics: When Medical Records Join the Web | Ninth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2010) at the International Conference on Knowledge Discovery and Data Mining, Washington, DC. | 2010 | published | |
| Fan Zhang, Mu Wang, and Jake Y. Chen* | Breast Cancer Plasma Protein Biomarker Discovery by Coupling LC-MS/MS Proteomics and Systems Biology | Proceedings of the ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY. | 2010 | published | |
| Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* | Random Walk Ranking Guided by Disease Association Networks for Lung Cancer Biomarker Discovery, | Proceedings of the International Symposium on Biocomputing, Vol. 1, No. 33, pp. 1-8. | 2010 | published | |
| Jieun Jeong and Jake Y. Chen | RIC: Ranking with Interaction Chains and its Applications in Computational Clinical Proteomics Studies | Proceedings of the International Conference on Bioinformatics & Biomedicine, pp. 216-221. | 2009 | published | |
| Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* | SWRWR: Seed-weighted Random Walks Ranking Method and Its Application to Leukemia Cancer Biomarker Prioritizations | IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 220-225. | 2009 | published | |
| Fan Zhang and Jake Y. Chen* | A Neural Network Approach to Multi-biomarker Panel Development Based on LC/MS/MS Proteomics Profiles: A Case Study in Breast Cancer, | Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems, pp. 1-6 | 2009 | published | 10.1109/CBMS.2009.5255456. |
| Hui Huang, Jiao Li, and Jake Y. Chen* | Disease Gene-fishing in Molecular Interaction Networks: a Case Study in Colorectal Cancer | Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | 2009 | published | |
| Xiaogang Wu, Ragini Pandey, and Jake Y. Chen* | Network Topological Reordering Revealing Systemic Patterns in Yeast Protein Interaction Networks | Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | 2009 | published | |
| Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Vaka, and Jake Y. Chen* | Visualizing a Correlative Multi-level Graph of Biology Entity Interactions | Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp.304-309. | 2009 | published | |
| John Springer and Jake Y. Chen* | Toward Ontology-Driven Omics Data Integration in Current Database Management Systems | Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp. 292-297. | 2009 | published | |
| Jiao Li, Pamela Crowell, and Jake Y. Chen* | Construct Anticancer Drug-Drug Correlation Network | Proceedings of the 24th Annual ACM Symposium on Applied Computing, Vol. 2, pp. 771-775 | 2009 | published | |
| Mingyi Wang and Jake Y. Chen* | Gene Selection using the GMM-IG Framework based Integrative Analysis. | IEEE Proceedings of the International Conference on Biomedical Engineering and Informatics, Vol.1, pp. 292-296. | 2008 | published | |
| Harini Kasamsetty, Xiaogang Wu, and Jake Y. Chen* | An Integrative Human Pathway Database for Systems Biology Applications. | Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1297-1301. | 2008 | published | |
| Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* | Mining Disease-Specific Molecular Association Profiles from Biomedical Literature: A Case Study. | Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1287-1291. | 2008 | published | |
| Jake Y. Chen*, Changyu Shen, Zhong Yan, Dawn P. G. Brown, and Mu Wang | A Systems Biology Case Study of Ovarian Cancer Drug Resistance. | Computational Systems Bioinformatics: CSB2006 Conference Proceedings, edited by Peter Markstein and Ying Xu, Series on Advances in Bioinformatics and Computational Biology, Vol. 4, pp. 389-398. | 2006 | published | |
| Jake Y. Chen*, Sarah L. Pinkerton, Changyu Shen, and Mu Wang | An Integrated Computational Proteomics Method to Extract Protein Targets for Fanconi Anemia Studies. | Proceedings of the 21st Annual ACM Symposium on Applied Computing, Dijon, France, Vol. I, pp. 173-179. | 2006 | published | |
| Jake Y. Chen*, Changyu Shen, and Andrey Sivachenko | Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data | Pacific Symposium on Biocomputing, Vol. 11, pp. 367-378. | 2006 | published | |
| Changyu Shen, Lang Li, Jake Y. Chen* | Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. | Proceedings of the IEEE Computational Systems Biology Bioinformatics Conference, Stanford University, Stanford, CA, Vol. 1, pp. 167-174 | 2005 | published | |
| Jake Y. Chen*, John Carlis, and Ning Gao | A Method for Conquering Complex Biological Database Queries. | Proceedings of the 20th Annual ACM Symposium on Applied Computing, Santa Fe, NM, Vol. I, pp. 110-114 | 2005 | published | |
| Jake Y. Chen* | Experience with Processing and Exploration of High-throughput Protein Interaction Data, Session on Systems Biology and Bioinformatics. | Proceedings of the Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, Vol. VII, pp. 41-45. | 2004 | published | |
| Jake Y. Chen*, Andrey Y. Sivachenko, and Lang Li | High-throughput Protein Interactome Data: Minable or Not? | High-throughput Protein Interactome Data: Minable or Not? | 2004 | published | |
| Jake Y. Chen*, Andrey Y. Sivachenko, Russell Bell, Connie Kurschner, Irene Ota, and Sudhir Sahasrabudhe | Initial Large-scale Exploration of Protein-protein Interactions in the Human Brain. | Proceedings of the IEEE CSB Bioinformatics Conference, Stanford University, Stanford, CA, published by IEEE Computer Society Press, pp. 229-234 | 2003 | published | |
| Jake Y. Chen* and John Carlis | Similar_Join: Extending DBMS with a Bio-specific Operator | Proceedings of the 18th ACM Symposium on Applied Computing, Melbourne, Florida, pp. 109-114. | 2003 | published | |
| Jake Y. Chen* and John Carlis | Managing Bioinformatics Challenges in Expression Microarray Sequence Selection Projects. | Proceedings of the Second Chinese Conference on Bioinformatics, Beijing, China. | 2002 | published | |
| Jake Y. Chen* and John Carlis | A High-density Microarray Case Study of Query Modeling In Bioinformatics. | Proceedings of the International Conference on Bioinformatics 2002, Bangkok, Thailand. | 2002 | published | |
| Yue Chen*, Libby Shoop, John Carlis, and John Riedl | A High-throughput System to Resolve Inconsistent Reading Frame Predictions for Expressed Sequence Tags. | Proceedings of Workshop on Inconsistency in Data and Knowledge at the International Joint Conference on Artificial Intelligence (IJCAI), Seattle, WA. | 2001 | published |
Conference Proceedings and Journal Special Issues
Books